PhysiCell is an open source 3-D agent-based simulator, suitable for simulating
millions of cells on desktop workstations.Author/maintainer:Paul MacklinProject site:http://PhysiCell.MathCancer.orgStatus: Native write support is in beta testing. Read support is planned. PhysiCell's internal
data structures are very similar to phenotype datasets and digital cell lines.

Tissue Simulation Toolkit is a cellular Potts modeling framework for simulating tissues.Author/maintainer:Roeland MerksProject site:https://sourceforge.net/projects/tst/Status: Full read and write support via the API have been implemented, with a release planned soon.

Image analysis

Software plugins for ImageJ are planned for release in 2017. This software will perform image segmentation
and output MultiCellDS digital snapshots.

Visualization and/or exploration

A talented team of undergraduate students at the University of Louisville, lead by
Hermann Frieboes, developed a first 3-D data visualization and exploration tool.
Further documentation is in the works, but Python code can be found at: